Sometimes when I shift down from a higher gear it simply wont click down and there is no resistance on the shifter. I think its a specific gear that has the issue since this never happened when shifting down from 6th gear. Its either 3, 4 or maybe 5.

It just happened again and I almost came to a stop but when I gave it gas it finally slipped into a gear and I could shift all the way down and speed up again.

So let me imagine, you're riding, pull the clutch lever, blip the throttle and shift down right?
Not coasting for a while with the engine at idle and then try to shift?

Also, when you downshift, when you release the clutch, are you still in the gear your were before you attempted to shift, or are you in a false neutral?

I wasnt coasting. I dont usually blip the throttle when shifting down. When I release the clutch it stays in the gear.

I used to have an issue with my Honda CB500 that would fall out of 2nd into neutral and other times would feel like a dead lever when trying to go into 3rd.  Turns out you really needed to toe it up hard.  Sometimes you'd get the gears to shift, but the shifter wouldn't actually click over so it would be this weird situation where you're in 2nd but the lever is in the neutral position.
I adjusted the lever down some so I had more range to lift, never was an issue after that, but I had to get used to pointing my toe down a little further to grab the lever.
Turned out to be a common issue with many riders, may have been a design flaw in the bike, but it was easy to overcome.

I wonder if you might be doing something similar in a higher gear with your GS.  If you are accelerating vigorously from a stop youll be shifting positively, and once you get to speed and relax you might be making a light shift.

Try this, but BE CAREFUL.  Have a friend help. 
Set her up on the center stand, you stand to the left of the bike, have someone on the right side holding the brake and the front end down.
Start it up and go through the gears by hand, no throttle but do clutch it.  If it's repeatable in this manner it might give you a better idea of what's going on.

Hi, I hope i'm not about to teach you to suck eggs! 
over time the clutch cable will stretch. This means that when you pull the clutch lever, you get a reduced action on the clutch actuator lever. You can make the required adjustment to allow for the stretched cable by removing the small cover on the left side of the engine casing, held on by two counter sunk screws.
once the plate is removed, hold the adjuster with a screw driver and slacken off the lock nut. screw the adjuster screw in until you feel resistance, then wind the screw back out about a 1/4 of a turn. Put the lock nut back on. as long as you have the correct amount of free play at the clutch lever, this should cure your problem.

Quote from: Countcoupe on October 29, 2016, 06:40:58 PM
You can make the required adjustment to allow for the stretched cable by removing the small cover on the left side of the engine casing, held on by two counter sunk screws.
once the plate is removed, hold the adjuster with a screw driver and slacken off the lock nut. screw the adjuster screw in until you feel resistance, then wind the screw back out about a 1/4 of a turn. Put the lock nut back on. as long as you have the correct amount of free play at the clutch lever, this should cure your problem.

I would adjust the lever before playing with the crankcase.  There's a procedure for this called the 3-point clutch adjustment.



But I don't think that's the issue here.  If the clutch was out of adjustment it would be hard to shift all the gears.